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Manganese in PDB 1kx5: X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution

Protein crystallography data

The structure of X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution, PDB code: 1kx5 was solved by C.A.Davey, D.F.Sargent, K.Luger, A.W.Maeder, T.J.Richmond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.950, 181.170, 109.490, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 27.5

Other elements in 1kx5:

The structure of X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Manganese atom in the X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution (pdb code 1kx5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 14 binding sites of Manganese where determined in the X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution, PDB code: 1kx5:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 14 in 1kx5

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Manganese binding site 1 out of 14 in the X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn3136

b:34.9
occ:0.72
 O J:HOH3212 2.1 31.9 1.0
O I:HOH3212 2.2 36.0 1.0
O I:HOH3771 2.3 42.0 1.0
O I:HOH3244 2.4 41.4 1.0
O J:HOH3175 2.4 32.8 1.0
O I:HOH3261 2.5 43.5 1.0
O J:HOH3332 3.9 53.6 1.0
O2 I:DT13 4.1 34.7 1.0
O I:HOH3292 4.1 51.6 1.0
O I:HOH3159 4.2 39.6 1.0
C2 J:DA-13 4.2 32.4 1.0
O4' I:DG14 4.3 36.2 1.0
N3 J:DA-13 4.4 32.7 1.0
O2 J:DT-12 4.4 34.5 1.0
O I:HOH3325 4.5 41.0 1.0
O4' J:DT-12 4.5 29.4 1.0
O I:HOH3245 4.5 38.6 1.0
C5' I:DC15 4.6 39.8 1.0
O4' I:DC15 4.6 42.6 1.0
C4' I:DG14 4.6 39.2 1.0
C4' I:DC15 4.7 45.5 1.0
C1' J:DT-12 4.8 32.0 1.0
N3 I:DG14 4.8 40.4 1.0
C4' J:DT-12 4.8 28.4 1.0

Manganese binding site 2 out of 14 in 1kx5

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Manganese binding site 2 out of 14 in the X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn3137

b:75.1
occ:1.00
 O I:HOH3306 2.3 43.5 1.0
O I:HOH3251 2.3 55.2 1.0
N7 I:DG48 2.5 57.5 1.0
O I:HOH3209 2.6 57.9 1.0
O I:HOH3193 2.7 49.5 1.0
O I:HOH3237 3.2 68.9 1.0
C8 I:DG48 3.4 54.4 1.0
O I:HOH3488 3.5 76.4 1.0
C5 I:DG48 3.6 56.7 1.0
O6 I:DG48 3.9 57.8 1.0
C6 I:DG48 4.1 57.8 1.0
OP2 I:DG48 4.2 61.0 1.0
C2' I:DT47 4.3 63.5 1.0
O6 I:DG49 4.4 53.7 1.0
O I:HOH3481 4.5 64.5 1.0
N9 I:DG48 4.6 56.6 1.0
C4 I:DG48 4.7 55.9 1.0
O J:HOH3460 5.0 63.7 1.0

Manganese binding site 3 out of 14 in 1kx5

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Manganese binding site 3 out of 14 in the X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn3138

b:61.9
occ:0.90
 O I:HOH3152 2.4 61.4 1.0
O I:HOH3181 2.5 55.8 1.0
O I:HOH3911 2.5 68.1 1.0
N7 I:DG61 2.5 62.0 1.0
O I:HOH3201 2.6 51.1 1.0
C8 I:DG61 3.5 62.5 1.0
C5 I:DG61 3.6 58.7 1.0
O6 I:DG61 3.7 52.2 1.0
C6 I:DG61 4.0 56.3 1.0
C8 I:DA60 4.1 58.6 1.0
N7 I:DA60 4.2 58.9 1.0
O I:HOH3242 4.2 58.5 1.0
O6 I:DG62 4.4 55.0 1.0
O J:HOH3338 4.5 58.5 1.0
O I:HOH3163 4.6 69.7 1.0
N9 I:DG61 4.7 62.6 1.0
C4 I:DG61 4.8 60.5 1.0
OP2 I:DA60 4.9 53.8 1.0
O I:HOH3789 4.9 67.6 1.0
N9 I:DA60 4.9 60.5 1.0

Manganese binding site 4 out of 14 in 1kx5

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Manganese binding site 4 out of 14 in the X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn3140

b:64.0
occ:0.72
 O I:HOH3259 2.4 52.1 1.0
N7 I:DG27 2.4 44.5 1.0
O I:HOH3243 2.6 62.2 1.0
O J:HOH3931 2.8 67.2 1.0
C8 I:DG27 3.4 44.0 1.0
C5 I:DG27 3.4 46.4 1.0
O6 I:DG27 3.6 53.3 1.0
O I:HOH3275 3.7 64.8 1.0
C6 I:DG27 3.9 46.9 1.0
O F:HOH291 4.2 86.3 1.0
C8 I:DA26 4.4 52.0 1.0
N7 I:DA26 4.4 51.2 1.0
O I:HOH3685 4.5 59.9 1.0
N9 I:DG27 4.6 45.1 1.0
C4 I:DG27 4.6 43.5 1.0
O F:HOH278 4.6 84.2 1.0
O F:HOH279 4.8 86.9 1.0
N4 I:DC28 4.8 48.0 1.0
OP2 I:DA26 4.9 63.7 1.0
O6 J:DG-28 4.9 58.2 1.0

Manganese binding site 5 out of 14 in 1kx5

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Manganese binding site 5 out of 14 in the X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn3141

b:44.6
occ:0.63
 O J:HOH3240 2.2 39.4 1.0
O J:HOH3152 2.3 43.2 1.0
O I:HOH3204 2.5 57.1 1.0
O6 I:DG5 2.5 37.5 1.0
C6 I:DG5 3.5 40.3 1.0
N4 J:DC-5 4.0 46.1 1.0
N7 I:DG5 4.0 44.4 1.0
N7 J:DG-6 4.1 36.7 1.0
O6 J:DG-6 4.1 33.8 1.0
C5 I:DG5 4.1 42.4 1.0
O I:HOH3887 4.2 77.5 1.0
O J:HOH3690 4.2 50.5 1.0
O J:HOH3415 4.2 73.7 1.0
O J:HOH3428 4.3 75.8 1.0
O J:HOH3595 4.3 50.9 1.0
O I:HOH3437 4.5 49.7 1.0
N1 I:DG5 4.7 38.7 1.0
C6 J:DG-6 4.8 36.0 1.0
C5 J:DG-6 4.8 34.6 1.0
O J:HOH3664 4.9 64.5 1.0

Manganese binding site 6 out of 14 in 1kx5

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Manganese binding site 6 out of 14 in the X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn3142

b:49.0
occ:0.64
 O I:HOH3333 2.4 61.0 1.0
N7 I:DG-3 2.5 36.2 1.0
O I:HOH3194 2.6 52.1 1.0
C8 I:DG-3 3.4 36.5 1.0
C5 I:DG-3 3.5 35.8 1.0
O6 I:DG-2 3.7 41.2 1.0
O6 I:DG-3 3.7 36.8 1.0
O I:HOH3429 3.9 90.4 1.0
C6 I:DG-3 4.0 33.8 1.0
O I:HOH3873 4.0 80.7 1.0
O I:HOH3256 4.0 38.4 1.0
O I:HOH3341 4.3 53.6 1.0
N7 I:DG-2 4.3 42.0 1.0
C6 I:DG-2 4.4 37.4 1.0
C2' I:DT-4 4.4 34.6 1.0
O A:HOH3331 4.5 61.2 1.0
O I:HOH3645 4.5 84.6 1.0
O J:HOH3734 4.6 54.5 1.0
N9 I:DG-3 4.6 37.3 1.0
C5 I:DG-2 4.6 40.8 1.0
C4 I:DG-3 4.7 35.7 1.0
O I:HOH3250 4.8 44.7 1.0
C6 I:DT-4 4.8 39.4 1.0
OP2 I:DG-3 4.9 26.9 1.0

Manganese binding site 7 out of 14 in 1kx5

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Manganese binding site 7 out of 14 in the X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn3143

b:69.4
occ:1.00
 O I:HOH3232 2.2 56.9 1.0
N7 I:DG-35 2.4 45.3 1.0
O I:HOH3319 2.5 66.5 1.0
O I:HOH3217 2.5 46.9 1.0
O6 I:DG-34 2.5 50.2 1.0
O J:HOH3933 2.7 70.9 1.0
C8 I:DG-35 3.3 41.2 1.0
C6 I:DG-34 3.4 47.1 1.0
C5 I:DG-35 3.4 44.6 1.0
O6 I:DG-35 3.7 47.9 1.0
N7 I:DG-34 3.8 45.6 1.0
C5 I:DG-34 3.9 47.4 1.0
C6 I:DG-35 3.9 46.2 1.0
O J:HOH3290 4.0 57.9 1.0
N4 J:DC34 4.2 63.3 1.0
O I:HOH3184 4.3 67.9 1.0
OP2 I:DG-35 4.3 48.8 1.0
C2' I:DT-36 4.4 49.9 1.0
N9 I:DG-35 4.5 45.1 1.0
N1 I:DG-34 4.5 44.5 1.0
C4 I:DG-35 4.5 44.2 1.0
O J:HOH3913 4.8 59.7 1.0
O3' I:DT-36 4.9 46.1 1.0

Manganese binding site 8 out of 14 in 1kx5

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Manganese binding site 8 out of 14 in the X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn3131

b:58.7
occ:1.00
 O J:HOH3430 2.4 60.0 1.0
O J:HOH3656 2.5 63.8 1.0
O J:HOH3274 2.5 54.6 1.0
O J:HOH3694 2.5 46.3 1.0
O J:HOH3221 2.6 53.8 1.0
N7 J:DG61 2.6 52.2 1.0
C5 J:DG61 3.6 50.4 1.0
C8 J:DG61 3.6 51.4 1.0
O6 J:DG61 3.6 48.1 1.0
O J:HOH3293 3.9 49.5 1.0
C6 J:DG61 3.9 52.0 1.0
C8 J:DA60 3.9 42.0 1.0
O J:HOH3485 4.0 50.9 1.0
N7 J:DA60 4.0 44.5 1.0
O J:HOH3351 4.1 51.0 1.0
O6 J:DG62 4.2 52.7 1.0
O I:HOH3428 4.5 49.7 1.0
O J:HOH3817 4.6 81.3 1.0
C4 J:DG61 4.8 54.2 1.0
N9 J:DG61 4.8 55.4 1.0
N9 J:DA60 4.9 43.9 1.0
OP2 J:DA60 4.9 38.6 1.0
O J:HOH3176 5.0 64.2 1.0
C5 J:DA60 5.0 44.1 1.0

Manganese binding site 9 out of 14 in 1kx5

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Manganese binding site 9 out of 14 in the X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn3133

b:51.9
occ:0.97
 O I:HOH3221 2.2 43.5 1.0
O J:HOH3208 2.2 51.3 1.0
O J:HOH3262 2.3 44.6 1.0
O J:HOH3209 2.4 53.8 1.0
N7 J:DG27 2.4 43.6 1.0
O I:HOH3158 2.5 61.6 1.0
C8 J:DG27 3.2 43.4 1.0
C5 J:DG27 3.6 49.0 1.0
O6 J:DG27 3.9 56.3 1.0
C6 J:DG27 4.1 49.8 1.0
O I:HOH3530 4.3 56.5 1.0
C8 J:DA26 4.4 48.5 1.0
N9 J:DG27 4.5 44.9 1.0
N7 J:DA26 4.5 49.2 1.0
OP2 J:DA26 4.6 59.9 1.0
O6 I:DG-28 4.6 56.9 1.0
C4 J:DG27 4.7 45.2 1.0
O I:HOH3414 4.8 51.5 1.0
O J:HOH3935 5.0 59.9 1.0

Manganese binding site 10 out of 14 in 1kx5

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Manganese binding site 10 out of 14 in the X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn3134

b:45.1
occ:1.00
 O J:HOH3307 2.3 42.6 1.0
O J:HOH3226 2.3 44.8 1.0
N7 J:DG-3 2.4 35.4 1.0
O J:HOH3917 2.5 43.5 1.0
O J:HOH3195 2.5 85.3 1.0
O J:HOH3169 2.5 55.4 1.0
C8 J:DG-3 3.3 35.4 1.0
C5 J:DG-3 3.4 35.2 1.0
O6 J:DG-3 3.7 35.9 1.0
C6 J:DG-3 3.9 35.9 1.0
O J:HOH3264 4.0 60.5 1.0
O J:HOH3275 4.2 47.1 1.0
C2' J:DT-4 4.3 28.9 1.0
O I:HOH3617 4.3 57.1 1.0
O6 J:DG-2 4.4 43.6 1.0
N9 J:DG-3 4.5 34.6 1.0
O J:HOH3632 4.6 75.1 1.0
C6 J:DT-4 4.6 35.4 1.0
C4 J:DG-3 4.6 36.0 1.0
C5 J:DT-4 5.0 32.9 1.0
OP2 J:DG-3 5.0 29.4 1.0

Reference:

C.A.Davey, D.F.Sargent, K.Luger, A.W.Maeder, T.J.Richmond. Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution J.Mol.Biol. V. 319 1097 2002.
ISSN: ISSN 0022-2836
PubMed: 12079350
DOI: 10.1016/S0022-2836(02)00386-8
Page generated: Sat Oct 5 11:24:28 2024

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